From 0a3fe7aeea76a8424da3a310fa8a8449cd4f28aa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Sat, 15 Apr 2023 12:35:24 +0200
Subject: [PATCH] Adapted `mf_narrow_summ' and `pack_ms2_w_summ' to new data
model.
Also adapted metfrag subsystem to new data model.
---
R/api.R | 2 +-
R/metfrag.R | 36 ++++++++++++++++++------------------
R/resources.R | 2 +-
R/shiny-ui-base.R | 5 +++--
R/state.R | 8 +++++---
5 files changed, 28 insertions(+), 25 deletions(-)
diff --git a/R/api.R b/R/api.R
index b29adef..239060c 100644
--- a/R/api.R
+++ b/R/api.R
@@ -783,7 +783,7 @@ metfrag <- function(m) {
path = m$run$metfrag$path,
subpaths = m$run$metfrag$subpaths,
db_file = m$run$metfrag$db_file,
- stag_tab = stagtab, ms2 = m$db$extr$cgm$ms2,
+ stag_tab = stagtab, ms2 = m$db$extr$spectra,
runtime=m$run$metfrag$runtime,
java_bin=m$run$metfrag$java_bin,
nproc = m$conf$metfrag$nproc)
diff --git a/R/metfrag.R b/R/metfrag.R
index cfab5a1..50d5cfc 100644
--- a/R/metfrag.R
+++ b/R/metfrag.R
@@ -36,7 +36,7 @@ metfrag_get_stag_tab <- function(summ) {
## Argument summ can be a subset of actual `summ' table.
x = gen_1d_keytab(summ)
data.table::setnames(x,old="key1d",new="stag")
- res = x[summ,`:=`(CE=i.CE,ion_mz=mz)]
+ res = x[summ,`:=`(ce=i.ce,ion_mz=mz)]
res
}
@@ -54,18 +54,21 @@ get_mf_res_ext <- function(fn) {
metfrag_run <- function(param,path,subpaths,db_file,stag_tab,ms2,runtime,java_bin,nproc = 1L) {
keys = intersect(colnames(stag_tab),colnames(ms2))
+ rms2 = ms2[stag_tab,on=keys,nomatch=NULL]
message("Generating MetFrag configs.")
- file_tab = ms2[stag_tab,{
+
+
+ file_tab = rms2[,{
r = write_metfrag_config(param = ..param,
path = ..path,
subpaths = ..subpaths,
db_file = ..db_file,
- stag = stag,
- adduct = adduct,
- ion_mz = ion_mz,
+ stag = first(stag),
+ adduct = first(adduct),
+ ion_mz = first(ion_mz),
spec = data.table(mz=mz,intensity=intensity))
- c(r,stag = stag)
- },by=.EACHI,on=keys]
+ c(r,stag = first(stag))
+ },keyby=keys]
message("Done generating MetFrag configs.")
withr::with_dir(path,{
@@ -89,21 +92,18 @@ metfrag_run <- function(param,path,subpaths,db_file,stag_tab,ms2,runtime,java_bi
mf_narrow_summ <- function(summ,kv,ms2_rt_i=NA_integer_,ms2_rt_f=NA_integer_) {
skey = data.table::key(summ)
- cols = c("adduct","tag","ID","CE","scan","mz","qa_pass","ms2_rt")
- nsumm = get_rows_from_summ(summ,kv,cols)
+ cols = union(names(skey),c("adduct","tag","ID","ce","precid","scan","mz","qa_pass","ms2_rt"))
+ dtkv = as.data.table(kv)
+ nsumm = summ[dtkv,on=names(kv),.SD,.SDcols=cols]
nsumm = nsumm[qa_pass==T] # Those that make sense.
- nsumm_key = union(SUMM_KEY,"ms2_rt")
+ nsumm_key = intersect(union(SUMM_KEY,"ms2_rt"),colnames(nsumm))
data.table::setkeyv(nsumm,nsumm_key)
- if (!is.na(ms2_rt_i)) {
- nsumm = nsumm[ms2_rt>(ms2_rt_i)]
- }
+ ms2_rt_i = if (!is.na(ms2_rt_i)) ms2_rt_i else 0.
+ ms2_rt_f = if (!is.na(ms2_rt_f)) ms2_rt_f else Inf
- if (!is.na(ms2_rt_f)) {
- nsumm = nsumm[ms2_rt<(ms2_rt_f)]
- }
+ nsumm[ms2_rt > (ms2_rt_i) & ms2_rt < (ms2_rt_f)]
- nsumm
}
get_metfrag_targets <- function(stag_tab,ms2) {
@@ -220,7 +220,7 @@ summarise_metfrag_results <- function(param,path,subpaths,cand_parameters,db_sco
}
.adapt_col_types <- function(x) {
- x[,(names(db_scores)):=lapply(.SD, as.numeric),.SDcol=names(db_scores)]
+ if (length(db_scores)>0) x[,(names(db_scores)):=lapply(.SD, as.numeric),.SDcol=names(db_scores)] else x
}
.calc_basic_scores <- function(x) {
diff --git a/R/resources.R b/R/resources.R
index 4cd7360..13688b4 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -217,7 +217,7 @@ FIG_DEF_CONF =list(grouping=list(group="adduct",
SUMM_COLS=c("set",BASE_KEY_MS2,"mz","ms1_rt", "ms1_int", "ms2_rt", "ms2_int",
"ms1_mean","ms2_sel",QA_FLAGS,"Name", "SMILES", "Formula", "known","Comments","file")
-SUMM_KEY = c("set","ID","adduct","tag","scan")
+SUMM_KEY = c("set","ID","adduct","tag","precid","catid","scan")
PLOT_FEATURES = c("adduct",
"tag",
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index a186eb4..03f5613 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1372,7 +1372,7 @@ mk_shinyscreen_server <- function(projects,init) {
fn = file.path(projdir,input$ms2_spectra_tab_name)
shinymsg(paste0("Saving MS2 spectra table to: ",basename(fn)))
tab2file(pack_ms2_w_summ(rvs$m$out$tab$summ,
- rvs$m$db$extr$cgm$ms2),
+ rvs$m$db$extr$spectra),
fn)
shinymsg("Done saving MS2 spectra table.")
})
@@ -1634,7 +1634,8 @@ mk_shinyscreen_server <- function(projects,init) {
path = rvs$m$run$metfrag$path,
subpaths = rvs$m$run$metfrag$subpaths,
db_file = rvs$m$run$metfrag$db_file,
- stag_tab = stagtab, ms2 = rvs$m$db$extr$cgm$ms2,
+ stag_tab = stagtab,
+ ms2 = rvs$m$db$extr$spectra, #rvs$m$db$extr$cgm$ms2,
runtime=rvs$m$run$metfrag$runtime,
java_bin=rvs$m$run$metfrag$java_bin,
nproc = rvs$m$conf$metfrag$nproc)
diff --git a/R/state.R b/R/state.R
index 157bbd9..309f83c 100644
--- a/R/state.R
+++ b/R/state.R
@@ -408,9 +408,11 @@ pack_ms2_w_summ <- function(summ,ms2) {
## Takes summ, finds entries with high quality spectra and subsets ms2 based on that.
## Take the columns we need from summ.
- x = summ[ms2_sel==T,.SD,.SDcols=c(key(summ),"mz","SMILES","Formula","Name")]
- mrg_keys = c(intersect(key(ms2),key(summ)),"scan")
- ms2[x,.(mz=i.mz,ms2_spectrum=encode_ms2_to_line(.SD[,c("mz","intensity")])),on=mrg_keys,by=.EACHI]
+ x = summ[ms2_sel==T,.SD,.SDcols=c(key(summ),"mz","SMILES","Name")]
+ mrg_keys = intersect(key(ms2),key(summ))
+ mrg_keys = c(mrg_keys,"scan")
+ ## ms2[x,.(mz=i.mz,ms2_spectrum=encode_ms2_to_line(.SD[,c("mz","intensity")])),on=mrg_keys,by=.EACHI]
+ ms2[x,.(ion_mz=i.mz,mz,intensity),on=mrg_keys,by=.EACHI]
}
--
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